Would a simple way to fix the country problem by having it as continents?
I do like the idea of virtual countries as well, as we could then get "balanced" teams

It appears that we have an unofficial UT2004 GoG server set up by Lyranaar/MarckY and SirDariusz so that might be a better bet than the UT99 edition I've contacted MarckY to see if he/she is interested in helping us set up a tournament (assuming we go for UT2004)